B. Nocek
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View article: Data collection from crystals grown in microfluidic droplets
Data collection from crystals grown in microfluidic droplets Open
Protein crystals grown in microfluidic droplets have been shown to be an effective and robust platform for storage, transport and serial crystallography data collection with a minimal impact on diffraction quality. Single macromolecular mi…
View article: Atomic-Resolution 1.3 Å Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE
Atomic-Resolution 1.3 Å Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE Open
We report the atomic-resolution (1.3 Å) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank…
View article: Indoline-6-Sulfonamide Inhibitors of the Bacterial Enzyme DapE
Indoline-6-Sulfonamide Inhibitors of the Bacterial Enzyme DapE Open
Inhibitors of the bacterial enzyme dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE; EC 3.5.1.18) hold promise as antibiotics with a new mechanism of action. Herein we describe the discovery of a new series of indoline s…
View article: Conservation of the structure and function of bacterial tryptophan synthases
Conservation of the structure and function of bacterial tryptophan synthases Open
Tryptophan biosynthesis is one of the most characterized processes in bacteria, in which the enzymes from Salmonella typhimurium and Escherichia coli serve as model systems. Tryptophan synthase (TrpAB) catalyzes the final two steps of tryp…
View article: Bisphosphonic acids and related compounds as inhibitors of nucleotide‐ and polyphosphate‐processing enzymes: A PPK1 and PPK2 case study
Bisphosphonic acids and related compounds as inhibitors of nucleotide‐ and polyphosphate‐processing enzymes: A PPK1 and PPK2 case study Open
Bisphosphonic acids, which are structural analogs of pyrophosphate, constitute a class of compounds with very high potential for the construction of effective inhibitors of enzymes operating on oligo‐ and polyphosphates. The bisphosphonate…
View article: Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases
Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases Open
Polyphosphate (polyP) kinases are widely conserved enzymes with importance in basic bacterial metabolism and virulence in many pathogens. However, the molecular mechanisms of their substrate specificity and catalysis remain unknown. Here, …
View article: Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters
Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters Open
The continuous growth of global plastics production, including polyesters, has resulted in increasing plastic pollution and subsequent negative environmental impacts. Therefore, enzyme-catalyzed depolymerization of synthetic polyesters as …
View article: Practical spectrophotometric assay for the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase, a potential antibiotic target
Practical spectrophotometric assay for the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase, a potential antibiotic target Open
A new enzymatic assay for the bacterial enzyme succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) is described. This assay employs N6-methyl-N2-succinyl-L,L-diaminopimelic acid (N6-methyl-L,L-SDAP) as the substrate with ninhydrin…
View article: Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism
Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism Open
The X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, t…
View article: Determinants and Prediction of Esterase Substrate Promiscuity Patterns
Determinants and Prediction of Esterase Substrate Promiscuity Patterns Open
Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequenc…
View article: Functional Characterization of Four Putative δ1-Pyrroline-5-Carboxylate Reductases from Bacillus subtilis
Functional Characterization of Four Putative δ1-Pyrroline-5-Carboxylate Reductases from Bacillus subtilis Open
In most living organisms, the amino acid proline is synthesized starting from both glutamate and ornithine. In prokaryotes, in the absence of an ornithine cyclodeaminase that has been identified to date only in a small number of soil and p…
View article: Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids
Exploring Bacterial Carboxylate Reductases for the Reduction of Bifunctional Carboxylic Acids Open
Carboxylic acid reductases (CARs) selectively reduce carboxylic acids to aldehydes using ATP and NADPH as cofactors under mild conditions. Although CARs attracts significant interest, only a few enzymes have been characterized to date, whe…
View article: Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families
Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families Open
Metagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different en…
View article: Biochemical and Structural Characterization of a Five-domain GH115 α-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T
Biochemical and Structural Characterization of a Five-domain GH115 α-Glucuronidase from the Marine Bacterium Saccharophagus degradans 2-40T Open
Glucuronic acid (GlcAp) and/or methylglucuronic acid (MeGlcAp) decorate the major forms of xylan in hardwood and coniferous softwoods as well as many cereal grains. Accordingly, the complete utilization of glucuronoxylans or conversion to …
View article: Structural and Biochemical Characterization of AidC, a Quorum‐Quenching Lactonase With Atypical Selectivity
Structural and Biochemical Characterization of AidC, a Quorum‐Quenching Lactonase With Atypical Selectivity Open
Quorum‐quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti‐infective agents in plants and animals. Herein, the st…